


Captain and Commander

by muldy



Category: Star Trek: Voyager
Genre: Angst, F/M, Romance
Language: English
Status: Completed
Published: 2017-01-19
Updated: 2017-01-19
Packaged: 2018-09-18 14:08:20
Rating: Teen And Up Audiences
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 1
Words: 4,549
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/9388631
Author URL: https://archiveofourown.org/users/muldy/pseuds/muldy
Summary: "Why? Why did it have to be him? With him everything was so simple, so easy. She never had to worry about taking a wrong step because he would be there to tell her that she had messed up. She didn’t have to worry that he wouldn’t speak to her because they disagreed, because he always respected her.But he was the most inappropriate choice for her.A Captain and her First Officer couldn’t fall in love."What was really happening behind the scenes from Season 1 to 4? Even a Captain has a few secrets.





	

**Author's Note:**

> I know I'm over 20 years late to this party, but I just discovered Voyager and I'm so completely heartbroken that Janeway and Chakotay don't get their happy ending in Endgame so I had to write something to make myself understand better.

She didn’t pay all that much attention the first time, it was just a mistake, a brush of hands against the console. That was easy enough to do, they shared the console after all.

It was during a Red Alert that she first paid attention to it. She was reaching for a button when his hand brush across the top of hers – but this time it stopped. She glanced up at him and felt the jolt. That familiar, unwanted jolt of excitement.

She shook off the feeling and looked back at the console, realising she hadn’t moved her hand.

He didn’t say it but she heard it.

_Everything would be okay._

She didn’t think about it again, but next time his hand lingered a moment too long, she let hers linger as well. It didn’t meant anything. She was just returning that comfort.

Reassuring him.

They didn’t have time for anything more in their circumstances.

 

*

 

It was on the Holodeck that she first saw him watching. She tried to ignore it at first, continuing her bland conversation with Neelix about some recipe he’d heard of from another planet. She didn’t need the attention, and she didn’t want it.

Or maybe she did. Maybe she was imagining it because she was lonely.

She glanced across at him again, and as though he knew she was watching he glanced away from Paris to look at her. This time he smiled and excused himself, walking towards her.

Part of her panicked. What would she say? Should she smile? Should she watch him walk over to him? Maybe he wasn’t, maybe he was just going to get another drink.

No.

He was walking straight for her.

‘So what do you think?’

Neelix’s voice shot through her consciousness like a phaser, completely pulling her out of her thoughts and making her acutely aware that she hadn’t been paying attention.

‘I think it sounds like a fantastic idea.’

She knew it was a risky response, but they had been discussing food right? And Neelix couldn’t possibly make anything worse…

‘Oh that is great, Captain! I’m very excited to make such an exotic dish for the crew.’

She was safe. It was food related. She smiled at Neelix and turned to leave, bumping straight into the person she was trying to escape from.

‘Drink, Captain?’ he asked.

Had he always been so physically impressive? He would look pretty good with his shirt off. Why hadn’t she noticed that before?

Oh god, it had been too long and her hope of ever seeing Mark again was starting to fade. That was all this was. Desperation. She was being an idiot. This was just Chakotay. She didn’t need to be nervous. He was her First Officer.

‘That sounds lovely, thank you Commander,’ she smiled.

He returned the smile.

Her heart jumped, just a little bit. He turned and she felt it fading quickly.

This was not ideal.

 

*

 

Sitting opposite him, their hands intertwined and his eyes looking straight through her she knew there was no hiding this anymore. And she had been the one to bring it up.

‘I – ‘ she started.

‘Kathryn,’ he cut her off, dropping their hands to the table and lightly running his thumb over hers. ‘We don’t have to finish this conversation now, we have all the time in the world.’

She took a deep breath before she spoke. ‘I know it sounds stupid because not only are we stuck in the Delta quadrant, we’re now stuck on this planet, but I have someone back home and I’m not sure I’m ready to let go of that yet.’

‘It’s okay,’ he whispered quietly. ‘When you are ready, I’ll be here. We have all the time in the galaxy.’

He squeezed her hand and smiled one more time before standing up. It was then she saw it, the flash of disappointment in his eyes as he turned away.

She stood up and walked around the table, grabbing his arm and pulling him back around,

‘Chakotay,’ she whispered. ‘How long have you felt this way?’

‘I don’t know. A long time,’ he whispered in response, reaching forward to touch her shoulder lightly.

They both let it hang for a moment, relishing the moment in case it died. She half expected her comms to go off, for something to interrupt, but the interruption never came.

His hand slid slowly closer to her neck, touching the spot where she had needed the massage earlier.

She let her eyes drop to his lips, right there, waiting for her. Then she looked back to his eyes, but too late. He’d seen it.

‘Kathryn, it’s okay,’ he whispered.

‘Stop saying that,’ she responded, not expecting it to sound so meek.

Where was her authority? She needed that right now to resist what she thought she was about to do.

‘How about I run you a bath,’ he dropped his hand slowly down her arm and let it come to rest on her hand.

She grabbed his hand in hers and gripped it tightly. He seemed surprised. She wanted this so much, but this part of her kept wondering if it was worth it, what if Voyager showed up tomorrow with some miraculous way to get home? What if Mark was still waiting for her back on Earth? What if…

Then it hit her.

What if they were actually stuck on this planet for the rest of their lives?

‘Kathryn?’

She leaned in and kissed him. He didn’t even hesitate before kissing her back, his hands instantly cupping her face, but it wasn’t overly eager, it was gentle, caressing.

Loving.

She pulled back.

Love.

Was she ready for that? Was this all because he was the only other person on this planet?

No, it was so much more than that.

He leaned in and kissed her lightly on the forehead.

‘There’s no rush,’ he whispered. ‘Goodnight, Kathryn.’

With that he turned and headed to his bed. She watched him go, and the moment she turned to walk to hers she let the smile spread across her face.

 

*

 

The door to her Ready Room opened and he walked in, then paused.

‘My apologies, I didn’t buzz in,’ he closed his eyes, realising what he’d done.

She smiled. ‘It’s okay Commander, just don’t make a habit of it.

He smiled in return but didn’t say anything, the doors closing behind him suddenly feeling like some kind of invitation. An invitation to walk over to him, to take his hand in hers, to –

The silence suddenly became very loud and she realised it was her turn to talk.

She’d forgotten, distracted by the memory of that kiss, the fact they thought they’d have forever, that feeling of disappointment the moment she had heard the word ‘Voyager’ coming from their comms.

‘How can I help you, Commander?’ she asked.

‘I was just wondering how you were?’ he said at the same time.

He took a few steps closer before taking a seat, not opposite her, but on her desk, leaning towards her.

‘I’m happy to be back on Voyager,’ she replied, carefully.

Her guard was up, she knew that. The temptation to say ‘Commander’ every time he spoke was strong, but she tried to push it away.

‘Kathryn – ‘ he started.

‘Chakotay,’ she cut him off. ‘We can’t. Not here.’

He considered her response for a moment, searching her eyes as though he was looking for something else.

‘You’re still hopeful we’ll get home,’ he spoke. ‘That you’ll see Mark again.’

An excuse.

That’s what he had been looking for.

She sighed, leaning closer to him and placing her hand over his.

‘I am the Captain of this ship, you are my second in command,’ she whispered. ‘Whatever I want to happen, it can’t.’

‘But you do want it,’ it was a statement.

She didn’t answer, she didn’t need to. They both understood.

He pulled his hand from hers and stood up.

‘I understand Captain, it’s not a problem,’ he said.

This time he turned before she could see the look in his eyes, but this time she didn’t need to. She felt it herself. As the doors shut behind him she had to push back the tears she didn’t realise she had in her.

 

*

 

‘I can’t let you do that, Kathryn.’

It wasn’t shouting but it was close. And they were in the middle of the Bridge.

And he had just used her first name instead of her rank.

It wasn’t that he never called her Kathryn, it’s just that he hadn’t done it before in front of the crew, in the middle of a Red Alert, on the bridge, while arguing loudly about how to save everyone’s lives.

She saw Paris and Kim exchange a look, Paris mouthing ‘Kathryn’ across the Bridge.

‘It’s not your choice,’ she put her foot down, then emphasized, ‘Commander.’

He suddenly realised what he had done, straightening himself up.

‘Captain, can I speak to you in your ready room please?’

‘Anything you need to say to me you can say right here,’ she was standing her ground.

He was silent for a few moments. Obviously he couldn’t say whatever he wanted to say and that was exactly what she wanted. She had made the mistake so it should be her to sacrifice herself. She wasn’t going to let him talk her out of it.

‘Let me go,’ he said quietly.

The panic struck her unexpectedly. She couldn’t let him go. She couldn’t let him do this to save her –

That was exactly what he had wanted. Without telling her how he felt he had just showed her and she wanted to hit him. She wasn’t going to let him win this, she was going to -

‘Captain,’ Paris interrupted. ‘They’ve gone.’

‘What do you mean gone?’

‘I don’t know, they just took off at Warp speed.’

There was silence for a moment.

‘Then I guess that is resolved,’ she said slowly. ‘Thank you Paris. Warp 8 out of here. I don’t want to risk them coming back with back up.’

She walked back to her seat and sat down. She didn’t watch but she could see him do the same in the corner of her eye, only he was watching her. She wasn’t going to bite, she wasn’t going to let him win this one.

 

*

 

The Holodeck boat was sailing quietly over Lake George, but the awkward silence between them was loud. It wasn’t stressful, in fact it was kind of comforting, but it was there and she couldn’t ignore it.

‘I heard a rumour,’ she smiled softly as she said it.

As always he returned the smile. ‘Oh you did, did you? And what would that rumour have been?’

‘I heard you were crying when they found you.’

She was a little more serious this time, but still trying to remain jovial. She didn’t want him to take it too seriously, but she also wanted to know if it was true.

He was silent for a moment, considering his response.

‘You mean a lot to me,’ his words were careful. ‘I can’t imagine doing this job without you by my side. And I most certainly don’t want your job if it means you aren’t here.’

‘So no apple off the head game then?’

She was still joking but he wasn’t. His smile had faded.

‘We never got to take that trip down the river,’ he said quietly, looking out over the lake.

That struck that chord, the same one she had felt the very first time she had considered him as anything more than a Commander and a friend. She hated that he could do that at any moment, say one thing and have her all flustered.

Although she had been the one to bring up the topic.

‘We’re almost doing it now,’ she responded.

He looked back at her. ‘Sometimes a part of me wishes we were still on that planet.’

Holding his eye contact with hers she reached forward and took his hand in hers. A week earlier she would never have admitted it, but she had seen her own death, her own funeral, she had almost died and she didn’t know if she was going to make it home.

This was her life now.

‘Me too.’

They stayed in silence for another half an hour, hands intertwined, pretending just for a moment, that they were back on that planet.

 

*

 

‘Are you avoiding me?’

She looked up as he sat down opposite her, some cold leftover food on his plate. It was late and there was no one else around but she hadn’t felt much like sleeping yet.

She tilted her head and smiled at him. ‘If I were I believe I would be doing a terrible job of it, given that we spent all day together.’

‘And yet you felt the need to avoid answering my question,’ he smiled in return and took a bite of his food.

He wasn’t being serious, but he also wasn’t going to drop the topic. A little part of her stomach began twisting itself into a knot as she watched him look down at his food and take another forkful. He looked back up at her as he ate.

Maybe she should just tell him.

‘You remember when Q came on board, because he wanted to mate?’ she asked.

He looked confused. ‘Yes, but that was months ago…’

Then he seemed to dawn on him, and the smile on his face spread wider. Then he laughed.

‘What’s so funny?’ she was almost offended.

Almost.

‘Is this about the holo-novel?’ his grin was still wide.

How was he always so good at reading her? She couldn’t hide anything. For a moment she looked away, suddenly realising how stupid the whole situation was, then found her smile spreading to match his.

He really did have a gorgeous smile.

Looking back at him she shook her head.

‘I know it’s stupid, to be jealous of a fictional version of Seska.’

He laughed. ‘I think you were just so attracted to the evil version of me that you couldn’t help but be jealous.’

‘You keep telling yourself that,’ she responded.

Although it was entirely true. There had been something extremely attractive about him going all rogue like that –

She closed her eyes, trying to push the image away.

Unsuccessfully.

‘Maybe if I’d continued my Marquis ways you’d be all over me.’

Her eyes flung open to look at him. His smile changed, reaching his eyes, but a complete calm took over his demeanour as he looked down to consider another bite of food.

She watched him while he wasn’t looking.

Why? Why did it have to be him? With him everything was so simple, so easy. She never had to worry about taking a wrong step because he would be there to tell her that she had messed up. She didn’t have to worry that he wouldn’t speak to her because they disagreed, because he always respected her.

But he was the most inappropriate choice for her.

A Captain and her First Officer couldn’t fall in love.

‘You’re still Marquis enough for me,’ she found herself saying, almost as though the words had taken control.

Or maybe it was her curiosity.

It was his turn to look at her in surprise, then the smile faded and he stood up.

‘I better get some sleep,’ he said quietly. ‘Goodnight Kathryn.’

‘Goodnight Chakotay.’

She watched as he left.

And then she stayed there another hour, drinking coffee and trying to push him from her mind.

 

*

 

She halted as they were walking out, focusing her attention on the floor. He turned to look back at her.

‘Kathryn?’ he asked.

His way of asking if she was okay.

‘I was using Mark as an excuse,’ she admitted.

She wanted him to know.

‘An excuse?’ he questioned.

‘To myself. For us to stay apart. I kept telling myself we might find a way to get home any day now and I could return to Mark that I would have to make the decision then.’

He was quiet for a moment before responding. ‘I see.’

‘It’s against Starfleet protocol, it’s distracting, it’s inappropriate,’ she paused for a moment, looking up at him. ‘But it’s what I want.’

The tension in the air dissipated immediately as he relaxed.

‘It’s what I want too,’ he responded.

‘Now what happens? What will it be, Chakotay? Hold fast to protocol? Indulge my feelings? What?’

She walked across the room to stand in front of him.

‘You have plenty of time to think about it.’

The smile that broke across her face was entirely involuntary, and was echoed by the look on his face. He held out an arm.

‘How about for tonight we head to the party and we deal with this tomorrow,’ he paused. ‘Or, whenever you’re ready.’

She hooked her arm through his. ‘I like the sound of that.’

 

*

 

She stood outside his quarters, waiting for the door to open. She had a suspicion that he had organised something sneakily for her, but she hadn’t expected it to be in his quarters.

Or maybe she was imagining things. Maybe he had just called her there to discuss work. After her shift. On her birthday.

The door opened to reveal him wearing his Marquis clothes.

She looked at him in slight confusion, then she remembered their conversation that late night months earlier and she smiled.

‘Planning a mutiny are you?’ she joked.

‘I thought it might be nice to get out of my Starfleet uniform for a few hours. Ignore protocol,’ he responded, taking a step back and holding his arm out for her to come in.

There was a single candle on the table, and a bottle of wine with two glasses.

She felt her heart swell in her chest, some kind of combination of panic and joy - the illogical, irrational, hopeful part of her wanting this to mean something.

And the logical, rational, fearful part knowing it did.

‘Chakotay, you didn’t have to,’ she spoke quietly, turning around to face him.

He was holding out a present. ‘Happy birthday.’

The panic subsided.

She opened it, revealing a beautiful watch.

Every fibre of her being was very aware of how close he was standing to her as he cupped his hands around hers.

‘It’s nineteeth century, mechanical movement. It’s a replica of the chronometer worn by Captain Cray of the British Navy. His ship was hit by a typhoon in the Pacific. Everyone back in England thought they were killed, but eight months later Crazy wailed his ship into London harbour. There wasn’t much left of it, a few planks, half a sail, but he got his crew home.’

She didn’t even know how to respond. It was the most perfect present anyone had ever given her. She wanted to hug him in response, to never let him go.

‘Chakotay…’ his name barely came out.

‘I love you, Kathryn.’

It was completely out of nowhere. Suddenly her ability to move, to speak, to breathe, disappeared. She didn’t know how to respond. After a few moments she saw the panic in his eyes as he let go of her hands and stepped back.

‘I didn’t mean to say that,’ he closed his eyes, letting out a deep breath.

‘I’m glad you did,’ she said quickly.

When his eyes reopened there was something new there. Determination. Hope. Desire.

‘I would wait until the end of time for you if I thought there was any chance at us happening,’ he said, stepping back towards her. ‘But it’s killing me, sitting next to you all day, wanting so much for us to cross that line and be more than anything I could have ever imagined and I need you to know that.’

She reached up and touched his face. ‘Chakotay, it’s okay.’

He reached his hand up and covered hers with it.

She wasn’t ready to say anything back but she wanted to thank him for saying it. She wanted to do far more than that…

‘Do you like the gift?’ he was trying to change the topic.

‘I love it,’ she responded.

And it was in that moment she felt it. It was now or it was never. And she wasn’t ready to make that decision.

So it had to be now.

She kissed him.

This time wasn’t tender, not like on the first time. This time he responded with years of built up sexual tension and need. His hands found their way up her arms, the watch dropping to the ground as she reached forward and began tugging at his shirt.

It had been a long time and god she wanted this.

And it was her birthday.

She paused.

‘Are you okay?’ he asked, concerned.

She smiled and relaxed. ‘I’ve never been better. But perhaps we should have drunk the wine first so we had something to blame tomorrow.’

He shook his head, leaning back in to kiss her again. ‘I don’t need an excuse.’

As his lips touched hers again any thought of command or Earth or Voyager or the Delta quadrant disappeared and the only thing that mattered to her was how quickly she could get his shirt off.

 

*

 

Paris was watching her, a suspicious look on his face.

‘Why are you so happy?’ he asked.

‘Is a Captain not allow to be happy the day after meeting a new race?’ she responded, still unable to fight her smile.

Paris still seemed suspicious, but decided to drop it. ‘Of course. I just haven’t seen you this happy about that before.’

‘Then I guess there’s a first time for everything, isn’t there?’ she returned her attention to the console.

Paris turned back slowly to pay attention to his work.

He entered the bridge at that moment, humming one of the tunes the Doctor was always singing in sick bay and looking straight at her. The jolt in her chest reminded her of exactly why she was so happy. Her eyes fell to his hands, those beautiful hands that had been all over her body the night before, his lips that had kissed every part of her, his Starfleet uniform that was covering up all the good bits…

‘Captain,’ he smiled. ‘Good morning.’

He took his seat, still humming, and pressed a few buttons on the console.

She glanced across at him.

‘Commander,’ she responded.

He made eye contact with her and winked as he did so. She felt herself turning red and hoped it was just her imagination. It couldn’t possibly be as obvious as it felt.

At that moment she saw Harry Kim out of the corner of her eye. He and Paris were exchanging glances again, except this time she knew.

They were seeing what shouldn’t be there.

The Starfleet Captain in her took over and she leaned back in her seat, looking ahead. This was such a bad idea.

 

*

 

‘Are you still awake?’ she asked quietly.

She hadn’t felt his arm go limp the way it normally did as he fell asleep, and given the fact it was wrapped very closely around her, his slow but not deep breaths echoing into her ear, she already knew that he was.

‘I was listening to you think.’

His voice in her ear ran down her spine like warm water, comforting her, although for once it wasn’t what she wanted.

She turned around slowly in the bed, facing him.

She reached up and touched his face lightly, running her fingers over his tattoo. He kissed her forehead as she did so.

‘Chakotay, we can’t keep doing this,’ she whispered.

He looked her in the eye and tightened his grip around her.

‘I know,’ he responded.

His voice wasn’t sad, wasn’t despondent, he knew it was the truth. That broke her heart even more than the idea of breaking it off with him.

She flattened her hand against his cheek, the tears doing their best to fight their way out of her eyes.

‘I love you.’

He already knew. She knew that. But if they were never going to discuss this again she needed to say it.

Their eyes searched each other and for a moment she wasn’t sure if they were going to ignore what had just been said and go back to sleep or if the conversation was going to continue.

‘I know,’ he smiled, but it was a sad smile. ‘And I would give almost anything to hear you say that every day for the rest of my life...'

He trailed off, running his hand down the side of her face.

‘But Voyager comes first,’ he finished.

She felt her heart breaking and realised she had never felt this before. Not in this way, not this agony and torture. This was something new and not in a way she had ever wanted to experience. It was as though someone had just reached into her chest and ripped out her insides.

She hadn’t expected the physical pain either, as though she had been punched, hard.

The worst part was this was her choice. If it were up to him -

Then the tears came and she began shaking, doing everything she could to stop any audible noise. The tears she couldn’t stop, but the rest she didn’t need him to see.

He pulled her in closer and held her until she cried herself to sleep.

When she woke in the morning he wasn’t there.

She didn’t leave her quarters that day.

She couldn’t let anyone see her like that.

 

*

 

‘Take these antacids twice a day, that should stop the pain.’

The Doctor was just trying to help, but it wasn’t going to make a difference. She knew the cause of her pain and it wasn’t anything physical. The Doctor must have been able to see that, he wasn’t an idiot.

‘And perhaps some time on the Holodeck. Relaxing,’ the Doctor continued.

She stood up to leave, noticing Chakotay standing at the other end of sick bay. The Doctor seemed to take his cue and walked off, pretending to be interested in something else.

‘You need alcohol, not antacids,’ he joked.

She half smile, half rolled her eyes.

She missed him.

Things hadn’t been the same and she missed everything about them. What she wouldn’t give for just one more moment with him…

‘I think all the alcohol is making the problem worse,’ she responded.

He smiled. ‘I’m glad to see you’re doing okay.’

She placed a hand on his arm. ‘Likewise.’

For a moment they hung there, stuck in the moment. It was then she realised this would never be entirely over. It couldn’t be. You didn’t just stop feeling that way about someone. It just had to wait.

‘ _Senior Officers to the bridge.’_

The announcement came over the speaker. It broke the moment and he took a step back, holding his hand out for her to lead the way.

‘After you,’ he spoke softly.

She took one last look into his eyes before heading out the door, him by her side.

No matter how much she wanted them to just be Kathryn and Chakotay, for now they were the Captain and the Commander, and they had a ship of people to get home.


End file.
